Removing gadolinium signal from T1 images?

AFNI Message Board
1

Hello -

I have a series of T1w volumes with gadolinium signal present…and I’m having difficulty registering them to an atlas volume (AFNI_18.0.26, auto_warp.py, MNI_T1_2009c+tlrc). Specifically, 3dQwarp seems to interpret the vessels as ‘brain,’ and wraps them around cortical folds. Is there any principled way to remove the gadolinum signal, while sparing brain?

Thank you,
Pete

2

I haven’t seen this myself, but I am perfectly willing to guess how to solve this.

  1. Use 3dQwarp’s exclusion mask -emask. You will need to create a mask image from just those voxels, maybe by thresholding and/or clustering.
  2. Smooth the vessels away with gaussian blurs.
  3. Hide the vessels by zeroing them out or reducing the intensities. For both this method and the previous one, you can still apply the warp to the original data.